Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LFNHPLCJ_2 | 232872 | 234041 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LFNHPLCJ_10 | 77486 | 78406 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| LFNHPLCJ_10 | 50686 | 52125 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| LFNHPLCJ_33 | 30920 | 33490 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LFNHPLCJ_3 | 9093 | 9947 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LFNHPLCJ_2 | 6774 | 7976 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| LFNHPLCJ_19 | 6571 | 6909 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| LFNHPLCJ_19 | 6254 | 6571 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LFNHPLCJ_10 | 974 | 1567 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| LFNHPLCJ_5 | 34599 | 35975 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.93 | 100.00 | X08034 |
| LFNHPLCJ_3 | 9095 | 9947 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| LFNHPLCJ_10 | 77486 | 78406 | mph(K) | Spiramycin, Telithromycin | 97.83 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LFNHPLCJ_5 | 34599 | 35972 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.78 | 100.00 | WP_003242953.1 |
| LFNHPLCJ_10 | 77489 | 78406 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| LFNHPLCJ_28 | 40188 | 41828 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| LFNHPLCJ_3 | 9096 | 9947 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LFNHPLCJ_5 | 37928 | 38446 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LFNHPLCJ_34 | 20955 | 23552 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 100.00 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| LFNHPLCJ_37 | 3320 | 4501 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LFNHPLCJ_17 | 11363 | 12148 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LFNHPLCJ_17 | 7527 | 8465 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| LFNHPLCJ_17 | 10141 | 11337 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| LFNHPLCJ_17 | 371 | 7507 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391076 |
| LFNHPLCJ_7 | 23854 | 24495 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| LFNHPLCJ_37 | 1695 | 2837 | capA | 0.0 | Capsule | Immune modulation | 98.86 | 100.00 | NP_391469 |
| LFNHPLCJ_15 | 22677 | 24440 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| LFNHPLCJ_37 | 2856 | 3305 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LFNHPLCJ_17 | 8493 | 10112 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| LFNHPLCJ_25 | 31891 | 33027 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LFNHPLCJ_51 | 4350 | 5219 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LFNHPLCJ_1 | 150324 | 151100 | CodY | 2.37e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LFNHPLCJ_4 | 66787 | 67356 | ClpP | 1.32e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LFNHPLCJ_13 | 51858 | 52250 | spxA1 | 5.14e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LFNHPLCJ_13 | 51858 | 52250 | spx | 3.07e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LFNHPLCJ_32 | 20841 | 21083 | SpoVG | 5.98e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LFNHPLCJ_7 | 35725 | 35919 | CspD | 8.65e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LFNHPLCJ_31 | 31265 | 31071 | CspB | 4.08e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LFNHPLCJ_1 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_2 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_3 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_4 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_5 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_6 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_7 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_8 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_9 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_10 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_11 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_12 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_13 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_14 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_15 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_16 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_17 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_18 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_19 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_20 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_21 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_22 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_23 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_24 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_25 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_26 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_27 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_28 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_29 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_30 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_31 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_32 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_33 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_34 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_35 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_36 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_37 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_38 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_39 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_40 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_41 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_42 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_43 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_44 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_45 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_46 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_47 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_48 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_49 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_50 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_51 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_52 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_53 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_54 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_55 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_56 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_57 | 1.0 | 0.0 | 1.0 |
| LFNHPLCJ_58 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_60 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_61 | 0.0 | 1.0 | 0.0 |
| LFNHPLCJ_63 | 1.0 | 0.0 | 1.0 |
| LFNHPLCJ_64 | 1.0 | 0.0 | 1.0 |
| LFNHPLCJ_65 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LFNHPLCJ_2 | 34812 | 58730 | False | Myoviridae | VOG7060, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| LFNHPLCJ_19 | 36390 | 62202 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| LFNHPLCJ_41 | 3982 | 24687 | False | Siphoviridae | VOG0787, VOG1638, VOG4552, VOG11060, VOG9600, VOG0025, VOG1884, VOG0198, VOG4841, VOG4556, VOG4581, VOG4544, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG3390, VOG4705, VOG0641 |
| LFNHPLCJ_42 | 17071 | 22973 | False | Unknown | VOG1292, VOG1309, VOG0083, VOG1878, VOG3549, VOG8241 |
Phigaro v2.4.0 (Database: Jan. 2024 release)